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Commits on Nov 5, 2013
  1. @joelarmstrong

    change halBlockViz lib to return target seq

    joelarmstrong authored
    (breaks existing code, but hopefully just the genome browser, since I
    renamed "sequence" to "qSequence.")
Commits on Nov 2, 2013
  1. Revert "dont run phylop on inserts in leaves. they will just be 0 any…

    authored
    …way"
    
    (I changed my mind.  We want those zeros.  Keeping them allows us to have fewer headers, which can be a bigger win in terms of size of resulting wigs and bigwigs)
    This reverts commit e789f92.
  2. remove logic where defaultValues were not lifted. this had the nasty …

    authored
    …side effect of creating lots of headers around zero values
Commits on Nov 1, 2013
Commits on Oct 31, 2013
  1. @joelarmstrong

    subtree conservation for halPhyloP (thanks Melissa)

    joelarmstrong authored
    and halPhyloP mask option fix
Commits on Oct 25, 2013
  1. @joelarmstrong

    deleted unneeded file

    joelarmstrong authored
  2. @joelarmstrong

    OS X Mavericks compatibility

    joelarmstrong authored
    (Benedict's code, closes #3)
Commits on Oct 22, 2013
  1. @joelarmstrong

    Fix wiggleLiftover segfault

    joelarmstrong authored
    (hopefully!)
Commits on Oct 16, 2013
  1. add --tab option and enable by passing a custom locale pointer to all…

    authored
    … functions reading bed streams
Commits on Oct 15, 2013
  1. @joelarmstrong

    Clarify column iterator usage

    joelarmstrong authored
    getColumnIterator expects position in sequence coordinates (genome coordinates if the sequence is a genome), but ColumnIterator->toSite expects the position exclusively in genome coordinates.
Commits on Oct 11, 2013
Commits on Oct 10, 2013
  1. @joelarmstrong
  2. @joelarmstrong
Commits on Oct 4, 2013
  1. @ngannguyen
Commits on Oct 2, 2013
  1. @ngannguyen
Commits on Oct 1, 2013
  1. @joelarmstrong
  2. @joelarmstrong
  3. fix typo in error message

    authored
Commits on Sep 30, 2013
  1. @ngannguyen
  2. Merge branch 'development' into lod

    authored
    Conflicts:
    	lod/halLodInterpolate.py
    	lod/impl/halLodExtractMain.cpp
Commits on Sep 29, 2013
  1. add missing includes

    authored
  2. change step parameter to scale in halLodExtract. this way different s…

    authored
    …ubtrees can get different steps
  3. @ngannguyen
Commits on Sep 27, 2013
  1. @ngannguyen

    Fixed indexing bug

    ngannguyen authored
Commits on Sep 26, 2013
  1. @ngannguyen
Commits on Sep 10, 2013
  1. @ngannguyen

    Fix track labeling

    ngannguyen authored
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